Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate Synpcc7942_0948 Synpcc7942_0948 permease protein of sugar ABC transporter
Query= reanno::Dino:3607127 (272 letters) >FitnessBrowser__SynE:Synpcc7942_0948 Length = 275 Score = 123 bits (308), Expect = 5e-33 Identities = 76/255 (29%), Positives = 135/255 (52%), Gaps = 7/255 (2%) Query: 24 PFYWMVTTSLKTQIVALEAPPV-WIFEPTLSNYREALFEDGVL--RTLINSLIIAISTTF 80 P W + TS+K P + W + T+ +Y +AL++ R L+NS +++ T Sbjct: 21 PILWQLLTSIKVNADIAAIPTIYWPRQWTVEHY-QALWQQTPAFGRYLLNSAVVSAIATL 79 Query: 81 LALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIARNLGLLDKHITLI 140 AL++G P A+A+AR R + L + + ++L + R L + + L+ Sbjct: 80 AALLIGTPCAYAIARRRDRSSQVLVGSLLLVTLFPYVLLFQGLLEVVRWLQWGNNYAALV 139 Query: 141 LIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGVAVSAIFS 200 + Y NLP+VI ++ F +P +L+EAA+++G S + I +PL P + + I + Sbjct: 140 VPYTALNLPLVILLLRSFFEQLPPELEEAAQIDGLSLGQRLWLILVPLTAPALVTAGILA 199 Query: 201 FIFSWNELMFGLILTRSEAKTAPAMAVSFMEG---YNLPYGKIMATSTLIVIPVLIFALI 257 FIFSWNE + L +A +AV+ + G +++PYG I A + + +P++ L+ Sbjct: 200 FIFSWNEYVLALSFISQQALKTVPIAVAEIGGISIFDVPYGDIAAATVVATLPLIGLVLV 259 Query: 258 ASKQLVRGLTMGAVK 272 A ++++ GLT GAVK Sbjct: 260 AQRRILEGLTAGAVK 274 Lambda K H 0.331 0.143 0.431 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 238 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 272 Length of database: 275 Length adjustment: 25 Effective length of query: 247 Effective length of database: 250 Effective search space: 61750 Effective search space used: 61750 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory